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Having a look at the "related search" feature to see why the index page has disappeared, i find that the page:
www.domain.com/?hop=0 has been index as the index page, which is an affiliate link.
The problem now is, how do I get this URL removed? Or get it re-directed to another URL?
Alternatively, I could just change the home page around, but there should be a way to remove a URL or re-direct from my own site.
Thanks in advance
You could add a disallow to your robots.txt file for that parameter format.
You could add a 301 redirect to your .htaccess to redirect those requests. This would also preserve the incoming PageRank too.
Your choice - each with different advantages and disadvantages.
If you block with robots.txt Google may still show it as a URL-only entry in the SERPs.
Additionally, Google will never see the meta robots noindex tag because they are banned from accessing the URL because of the robots.txt disallow rule.
Only the robots.txt and the redirect stop the URL from being listed. Only the redirect passes PageRank over.